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RMapDB: chemical reaction route map data for quantum mechanical-based data chemistry

Hiroko Satoh1,2*, Tomohiro Oda3*, Kumiyo Nakakoji4*, Takeaki Uno5*, Satoru Iwata6*, Koichi Ohno7,8*

1 Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland

2 Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan

3 Software Research Associates Inc., Tokyo 171–8513, Japan

4 Department of Media Architecture, Future University Hakodate, Hakodate, Hokkaido 041-8655, Japan

5 National Institute of Informatics (NII), Tokyo 101-8430, Japan

6 Department of Mathematical Informatics, The University of Tokyo, Tokyo 113-8654, Japan

7 Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980–8578, Japan

8 Institute for Quantum Chemical Exploration, Konan 1-9-36, Minato-ku, Tokyo 108–0075, Japan

* Corresponding authors emails: hiroko.satoh@chem.uzh.ch, tomohiro@sra.co.jp, kumiyo@fun.ac.jp, uno@nii.ac.jp, iwata@mist.i.u-tokyo.ac.jp, ohnok@tohoku.ac.jp
DOI10.24435/materialscloud:5f-14 [version v1]

Publication date: Nov 04, 2020

How to cite this record

Hiroko Satoh, Tomohiro Oda, Kumiyo Nakakoji, Takeaki Uno, Satoru Iwata, Koichi Ohno, RMapDB: chemical reaction route map data for quantum mechanical-based data chemistry, Materials Cloud Archive 2020.138 (2020), doi: 10.24435/materialscloud:5f-14.

Description

The record contains quantum mechanical (QM) global reaction route map (r-map) data. R-map is chemical reaction pathway networks, which compose equilibrium (EQ) and dissociation channel (DC) and transition state (TS) structures connected via intrinsic reaction coordinates (IRC) obtained by QM calculations. These are contents of RMapDB, which was published first in 2010 as a prototype and has been available online since 2014. The record contains global r-maps of three- to five-atom molecular systems. It contains also a conformational r-map of alpha-D-glucose and a global r-map of C2H4O2, which were discussed in potential energy surface-based conformational analysis and three-dimensional substructure search with the general root mean square deviation (G-RMSD) method. The RMapDB database has been developed in the RMap project for data chemistry based on QM chemical reaction route maps, together with an analytical tool RMapViewer and a server system RMapServer.

Materials Cloud sections using this data

No Explore or Discover sections associated with this archive record.

Files

File name Size Description
ReadMe.yaml
MD5md5:7f121b6ffc96892ad33f95016aaf5c7c
25.4 KiB Descriptions about contents (yaml)
data.tar.gz
MD5md5:9eebe4390782f6e95e6e51a100252e19
32.0 MiB Data archive (tar.gz)

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution Non Commercial Share Alike 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Website (Conference proceedings where the database (RMapDB) is described.)
Website (Conference proceedings where the database (RMapDB) is described.)
Journal reference (Paper in which the database (RMapDB) is described.)
Journal reference (Paper in which the data is discussed.)
Journal reference (Paper in which the data is discussed.)
Website (Webserver where the data can be searched.)
Software (Software to visualize the data.)
Software (Software to build a database for the data.)

Keywords

chemical reaction pathway global reaction route map transition states intrinsic reaction coordinates ab initio DFT HF RMapDB RMapViewer RMap project G-RMSD Glucose Maizo

Version history:

2020.138 (version v1) [This version] Nov 04, 2020 DOI10.24435/materialscloud:5f-14